Legendary War
by Kamotz
Summary: Millenia after a war that nearly ended the world, the balance between humans and Pokemon is about to shatter, and a war will rock the world as never before. IN PROGRESS OF BEING REWRITTEN!
1. Prologue: Tome of War

(A/N): This is my first Pokemon fanfic. But I really like the way it's turning out. I think it definitely takes a different direction than other Pokemon fics; it's a little darker and more mature. It deals with death and all that, but still has the classic (almost childish) "I wanna take over the world" theme in the background. While this story may start out slow it quickly jumps to a fast-paced style. At times I think it gets a little too fast, too quickly but it does go back to a bearable "tempo". Anyway, **I don't own anything but the storyline**. Please R&R and enjoy.

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Prologue: Tome of War**

_In ancient times, long before the dawn of civilization, a great war raged across the planet. But it was not a war between humans. This was a war between Pokemon. No one knows why the war began or who started it, but the war almost destroyed the world._

_What is known is that the battle was fiercest between Groudon and Kyogre. Their own personal duel eventually came to dwarf the rest of the war. The war finally began to subside, but the battle between the two giants did not. Groudon and Kyogre continued their battle even as the world around them shattered in their wake. Entire mountains were uprooted and oceans evaporated. Continents rose above and sunk beneath the waves all within a matter of hours. It seemed as if their battle would destroy the world._

_Salvation seemed to arrive with the appearance of Rayquaza and his two heralds –Latios and Latias. Rayquaza succeeded in pacifying Kyogre and Groudon -sending them into a deep slumber. But soon he himself was gripped with an unquenchable thirst for battle and destruction. Together with his two heralds, Rayquaza then managed to defeat both Lugia and Ho-oh._

_All seemed lost until the diminutive Mew arrived. Using her vast psychic power, Mew was finally able to put a stop to Rayquaza by calming the mighty dragon's mind. Disgusted by his actions, Rayquaza flew high into the sky and was rarely seen again. His two heralds -Latios and Latias- flew off together towards isolated islands. _

_But it was far from over. The radical changes in climate had led to the extinction of countless Pokemon species and had almost eradicated the humans as well. Much work had to be done to ensure the survival of the planet's life so tasks were divided up among the remaining legendary Pokemon. Articuno, Zapdos, and Moltres –otherwise known as Lugia's Coven- were assigned the task of watching over the skies of the world. Lugia himself would in turn watch over the seas and oceans. Entei, Raikou, and Suicune –otherwise known as Ho-oh's Coven- would become the watchers of the land and Ho-oh herself would watch over the growth of humanity. Mew was tasked with watching over the world as a whole and would respond to aid it in times of great crisis. Regirock, Regice, and Registeel became the guardians and messengers of Mew, protecting her when need be. Celebi became the watcher and guardian of time itself. Her task was to protect the flow of time while also looking into the near future for potential threats. Jirachi however, had mysteriously vanished during the war's end. Many believed that he had been destroyed._

_And slowly, slowly the legendary Pokemon that guarded the world began to drift away from the sight of the humans and Pokemon that they protected. They began to watch from afar as humans began catching and training Pokemon for battle, knowing that they could not afford to be caught. But humans would often get a glimpse of the Legendaries and this would inspire them to try and capture them, for either their own selfish gain or for scientific research. And yet the Legendaries remained distanced from mankind._

_And for hundreds upon hundreds of years, the balance was perfect. Until humans started to get clever, that is. The creation of Mewtwo threw the hard-kept balance completely out of sync. Until that point, Mew was considered by some to be the most powerful of the Legendaries, and was certainly the most powerful psychic. But Mewtwo surpassed her in both aspects. Thankfully however, Mewtwo was not interested in upsetting the balance and he eventually was willing to let the world be in peace._

_The actions of a human also caused the great catastrophe between Lugia and his coven. The capture of the three Legendary Birds almost lead to the capture of Lugia, and the world was nearly destroyed during their battle. But thankfully, the crisis was averted and the balance was restored._

_The arrival of Deoxys seemed to be the event that would destroy the balance; his arrival even caused Rayquaza to return to the planet's surface to attempt to redeem himself by defending the planet. But in the end, Deoxys was happy to return to outer space._

_And so the fragile balance between the Legendaries, the humans, and the Pokemon was preserved._

_Until now, that is…_

_A being eons old has emerged from deep under the planet's surface. He calls himself the "God of all Pokemon". His power shields his presence from the Legendaries and he now freely walks the world, gathering followers –both human and Pokemon alike- forming a secret cult-like society. In addition, he has the power to call upon his force of twisted "Dementia Pokemon", convert others' Pokemon into the "Dementia" type, and bring all but the most powerful psychics under his control. His goal is to bring the world fully under his control and he seems quite capable of doing so. Only the Legendary Guardians stand in his way._

_To make matters worse, Deoxys has returned with a malevolent agenda of destruction that sweeps across the world. His return has triggered the revival of age-old conflicts between the Legendaries as tempers flare and rationales dwindle. The so-called "God of all Pokemon" will undoubtedly use this to his advantage, for once all the Legendaries are defeated; his rise to power will be assured._

_All is not lost, however. The Pokemon League has called together some of its most powerful and dedicated members in an attempt to stop the so-called "god". But it will not be easy, for his influence knows no boundaries and his cause has already brought many other members of the Pokemon League to him, and Deoxys provides a second front to distract the enemies of the "god"._

_The world's only hope may rest in the actions of a handful of trainers, and in the power of the Legendaries. This is their story…_


	2. Chapter 1: Warriors Gather

**Disclaimer:** I do not ownPokemon or any of the characters.

(A/N): Well the first real chapter is up. The "prologue" was more of an introduction to this alternate world of Pokemon. This story will have absolutely nothing to do with Ash or any of the characters from the show. This story will only have the game incarnations of characters. Read on and you'll understand. Reviews of all types are appreciated. R&R. Enjoy.

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**Chapter 1: Warriors Gather**

Lance the Dragon Master, the leader of the Kanto Elite Four waited in the meeting room with a forlorn expression on his face. The champion and leader of the Hoenn Elite Four, Steven, wore much the same expression. Before them in the massive meeting room sat various Gym Leaders from Kanto, Johto, and Hoenn as well as a few members of each region's Elite Four.

"I'm glad you all could make it," Lance began. Lance was a man of average height, but his eyes shone with intensity. "I'm sure many of you have noticed that not everyone is here, and that is what Steven and I have called you here to discuss." Lance nodded for Steven to continue.

"As you may or may not be aware of, it has recently come to our –mine and Lance's- attention that there is a secret cult that is growing around the three regions at an enormous rate," Steven said. Steven was around Lance's height with silver-white hair. He was cleanly dressed and had a wealthy air about him.

"I've heard of this thing," Flannery –the Gym Leader of Lavaridge Town- spoke up. She was a young woman with long red hair. "The leader of the cult is some guy claiming to be a Pokemon god or something, right?"

Lance nodded. "This is highly –and I'd like to stress highly- unlikely," he said. "But nevertheless this man has assembled a very large following. Many members of the Pokemon League have joined him as well."

"In fact," Steven said. "Those Gym Leaders and members of the Elite Four that you don't see here have more than likely joined him."

"You know," Lieutenant Surge –the Gym Leader of Vermillion City- said. He was a large, powerfully built man with spiky blonde hair. "I ain't too surprised at all about Giovanni joining this creep, but Koga and Blaine? That's just a little hard for me to swallow."

Pewter City's Gym Leader, Brock, nodded his agreement. Brock was a dark-skinned young man with narrow eyes and black hair. "Yeah, something doesn't seem right. I mean Koga, Blaine, and even Giovanni have such strong personalities. I can't picture any of them being drawn into a cult."

"Well, all surprises and disbeliefs aside," the Blackthorn City Gym Leader, Clair, said. "With Giovanni on his side this so-called 'god' will have the nearly unlimited resources of Team Rocket at his disposal."

"Listen, we don't really know if Giovanni is the head of Team Rocket," Lance interjected.

"Lance," Lorelei, a slender, beautiful brunette and Lance's fellow member of the Kanto Elite Four, objected. "You know that truth better than any of us."

"Whether Giovanni is or isn't the leader of Team Rocket isn't the case here," Steven said, finally putting an end to the discussion. "Our problem is that some wacko claiming to be a god has successfully recruited six Gym Leaders, two members of Hoenn's Elite Four, a former Elite Four member from Kanto, and the current Hoenn League Champion."

"Wallace?" Flannery gasped. "How did this nutcase manage to convince Wallace to join him?"

"That's what we want to find out," Lance stated.

The Gym Leader from Ecruteak City –Morty- stepped forward. He was a tall young man with long blonde hair held back by a sweatband. "Just so we're not left in the dark," he said. "Can you tell us who exactly this nut-job has recruited?"

Lance nodded. "Aside from Wallace, this guy has managed to bring Karen into his fold. Karen was a member of Kanto's Elite Four while Lorelei and Agatha were away. She specializes in Dark-type Pokemon."

"From the Hoenn Elite Four, both Sidney the Dark Master and Drake the Dragon Master have joined him," Steven informed. "You've heard about Giovanni, Blaine, and Koga joining him from their gyms in Viridian City, Cinnabar Island, and Fuchsia City respectively."

"Juan, the Sootopolis Gym Leader and Wallace's old mentor has also joined them," Lance said. "From Johto…Chuck and Pryce, the Gym Leaders from Cianwood City and Mahogany Town have joined as well."

"Those are some heavy-hitters that this guy's got on his side," said the Kanto Elite Four Fighting Master, Bruno. "But honestly, what can we do about it? I don't think that they're doing anything illegal by joining a 'club', are they?"

"I just want us to be sure," Lance said. "This guy, this 'god', is not a particularly sane guy. He's out there preaching the 'take over the world' thing like some lame Saturday morning cartoon villain."

"Normally we wouldn't worry about something like this," Steven said. "There's been dozens of crazies out there trying to take over the world with nothing but a misfit band of kids and a handful of half-dead Pokemon. But this guy has official members of the Pokemon League with him, almost enough to create a league of his own."

"And you want to know why this guy is so different from the rest, don't you?" Koga's daughter Janine asked. "You want to know why this guy was able to convince people like my father to join him."

"Exactly," Lance nodded. "Why is this guy so great? What has he offered them? What dirt does he have on them? Has he threatened them? These are the things we need to know."

"So why just us?" Bruno asked. "Why have you called only ten of us here? Why not call in the entire League?"

"Because then they'll know that we're on to them," Steven answered simply. "We called you all here because we know we can trust you. Brock and Misty, your loyalty to the League has been very well documented. Lieutenant Surge, your combat experience would be an invaluable asset. Sabrina, your psychic powers might give us a distinct advantage to tell if people are lying. Janine, apart from the possibility of you being able to get through to your father, you are also a skilled ninja, and your reconnaissance abilities would come in handy. Flannery, Morty, and Clair, the three of you have constantly proven to be worth and dedicated Gym Leaders. And Lorelei and Bruno, your skills as members of the Elite Four are unmatched."

"But this 'god' isn't our only problem," Lance stated dejectedly. "There have been some strange occurrences all over the world. For the past few weeks, I've been receiving reports about a strange Pokemon that attacks towns and cities seemingly at random."

"Why don't the local authorities or Gym Leaders handle this thing then?" Misty asked.

"That's the thing," Lance sighed. "By the time the authorities or Gym Leaders arrive, this Pokemon –whatever it is- has already destroyed half the city and has vanished."

"So has anyone ever gotten a good look at this thing?" Clair asked. "Does anyone know what it is?"

"Yes and no," Lance answered cryptically. "I'll explain. Two days ago the creature appeared in Petalburg City and began its rampage. However, unlike in the other cities, this time the local Gym Leader, Norman was able to engage it in battle." Lance paused and looked each of his fellow League members in the eye. "Now I'm sure you know that Norman is no pushover, but this strange Pokemon defeated him and his Pokemon in less than a minute before flying off at what Norman called 'impossible speeds'."

"So does Norman know what it is?" Brock asked. "Can't he tell us what's been destroying all these cities?"

"See, therein lays the problem," Lance sighed. "Norman said he had never seen anything like it before in his entire life. I mean, there's legendary Pokemon and rare Pokemon, but Norman says that this was like something completely foreign."

"Did he describe it?" Morty asked. "What did it look like?"

"He said it was very slender," Lance answered. "It was green and red, had four tentacles for arms, had a strange t-shaped head, and had a glowing purple jewel in the center of its chest."

"Do you think its connected to our loony 'god'?" Steven asked.

"Maybe," Lance sighed. "Or it might just be some coincidence. This Pokemon –if it is a Pokemon- has been attacking at random. It goes from one region to another. It might be on Johto one night, and in Hoenn the next morning."

"So what do we do?" Janine asked.

"If it attacks again, I will know," Sabrina answered. The powerful psychic finally stepped forward and spoke. "Once I find where it is I'll have one of my Pokemon use _Teleport_ and I'll get to it and try to continue to follow it."

Lance nodded. "Not a bad idea," he agreed. "But don't get in over your head. We need you back here so your safety is our prime concern."

"Do we have any idea where it might head next?" Lorelei asked. "Any idea at all?"

"I have absolutely no clue," Lance answered tiredly…


	3. Chapter 2: Love and Loss

**Disclaimer:** I do not own Pokemon or any of their characters. I do however claim ownership of my variations of the characters Red and Blue.

(A/N): Here's where the main human protagonists will be introduced. Yes Red and Bluewere slightly influenced by the games and yes I could have come up with better names for them, but I chose to do it this way. Reviews are appreciated. R&R. Enjoy.

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**Chapter 2: Love and Loss**

Red lounged lazily on a lawn chair as the clouds slowly moved overhead. The seventeen year-old Pokemon trainer yawned and stretched his arms before placing them behind his head. He sighed contently as he felt the wind slowly flow over his body, lightly ruffling his black hair. He was dressed in kaki shorts, a white, sleeveless muscle shirt, and a button-down, red, palm tree printed shirt. They were the perfect clothes for the ancient and powerful art of sunbathing.

"This is the life," Red yawned as he reached for his glass of water. "No Pokemon battles, no crazy Team Rocket, just some good 'ole R and R." He went for his water but came up empty handed. "What the-?"

"You know, you're really getting lazy these days," Blue said as she took a gulp of Red's water. "If you're not careful, someone is gonna' come by and beat you," she warned. Blue was Red's age with long, straight, dark brown hair and bright green eyes. She was wearing a black mini-skirt and a bright green tank top.

"Thanks 'mom'," Red growled sarcastically. "How 'bout you give me my water back and quit botherin' me." He held out his open palm, waiting for the return of his water glass.

"Have your stupid water," Blue said with a huff and poured the water onto Red's head. She smirked proudly at her achievement.

Red was shocked at first but then quickly shrugged his shoulders and settled back down. "You know you only did that to see me soaking wet," he said with a grin. He continued with his tirade. "I mean it's not that big of a deal. Just admit that you're attracted to me. It would be a good thing to get that out in the open. It's not healthy to keep that all bottled up inside."

Blue sent Red an incredulous look. "You must be out of your mind!" she shrieked, completely red-faced and flustered. "Of all the inconsiderate, chauvinistic, pig-headed things you've ever said, _that_, Red must have been the most-"

Something shiny flashed in the corner of Red's eye while Blue was screaming at him and suddenly Red had only seconds to react. He quickly dove onto Blue and carried her to the ground an instant before the house across the street exploded.

"What the hell?" Blue screamed as the debris landed all around them. Red looked towards the sky and was able to make out a dark form floating in the air high above them. A burst of light flashed from the figure.

"Move, now!" Red yelled. He dragged Blue to her feet and they started to run just as Red's house (where they had been moments before) exploded as well. The shockwave sent the two tumbling to the ground.

"What happened?" Blue asked. She coughed as the smoke from the burning houses drifted towards her. But Red wasn't paying attention. His attention was focused on the strange figure that had landed amidst the rubble.

"That happened," Red said as he pointed towards the strange creature. It was green and red, with four tentacles and a strange shaped head. A large purple jewel glowed at the center of its chest. But the strange creature didn't even acknowledge Red and Blue's existence. It simply glanced to another house and destroyed it, seemingly without effort.

"Bastard!" Red roared. He reached to his belt and grabbed a Pokeball. "Poliwrath, kick his ass!" Red chucked the ball forward and his Pokemon emerged in a flash of light.

The blue and white tadpole Pokemon nodded to Red in affirmation and charged towards the creature. But the invader was unconcerned by its attacker's presence. Without even looking towards Poliwrath, the creature struck. It grabbed Poliwrath with its two left tentacles and held its adversary securely in place. But with a quick yell from Red, Poliwrath blasted the creature with a powerful water attack.

The strange creature, however, did not relinquish his hold. Instead, he slowly turned his head to the struggling Poliwrath, and his deep soulless eyes bored into Poliwrath's own. Power and energy suddenly burst from the creature's eyes and struck Poliwrath, vaporizing the entire left side of the poor Pokemon's body.

Deoxys dropped the now-lifeless Pokemon as Red stared at the corpse with wide-eyed disbelief and horror. Without warning, Deoxys then blasted off into the sky, flying away with amazing speed…

**----------Interlude: Three hours later----------**

Red stood over the fresh plot of soil as the small headstone was erected. Blue stood next to him, a somber look on her face. Around them, firefighters struggled to put out the last remaining fires. Professor Oak silently walked up beside Red.

"I've brought you your Nidoking," the professor stated, offering Red a Pokeball. "Just as per your request."

"Thanks," Red muttered as he took the ball containing his Nidoking and switched it with the now-cracked ball that once held his Poliwrath. Red struggled to keep his composure as he knelt down and buried the broken Pokeball with his former partner. Red stood up and glared toward the setting sun, to the direction where Deoxys flew. "I'm going to find that thing."

"Of this I have no doubt," Professor Oak said. "Just be careful."

"I'm going to find that monster," Red swore with tears in his eyes. "And when I do…I'm going to make it regret every minute of its miserable life." With those words Red turned and left to prepare.

He walked through the charred remains of his home and managed to find a change of clothes. He was wearing the same white muscle shirt but now wore black pants and a plain, blood red button-down shirt with the sleeves rolled up. He shrugged his backpack onto his shoulders and stepped out the door only to be greeted with the sight of Blue –also in changed clothes- waiting for him.

"You're not going alone," she said forcefully, while looking into his eyes. "I'm coming with you."

Red stared her down for a few more seconds but then realized that nothing he said would make her do otherwise. "Fine," he muttered. "But don't get in my way." Red moved to step past her when she flung her arms around his neck and pulled him into a tight hug. Red allowed his head to drop as a single tear ran down his face.

Blue suddenly jumped back in embarrassment. While she stuttered to find an explanation Red gently placed a hand on her shoulder. "Let's go," he whispered gently but with conviction. Determination shone in the young man's eyes as he glared into the setting sun…

**----------Interlude: With the Elite Four----------**

"I've located it," Sabrina blurted out. "The creature that Norman battled. It attacked Pallet Town a little while ago and was been moving too fast for me to get a fix on it until just now."

"Wait," Lance said. "Did you just say 'Pallet Town'?"

Sabrina nodded. "It attacked the town around noon today and engaged in battle with one of the local trainers named 'Red'."

Misty had a pensive look on her face. "Come to think of it, wasn't there a 'Red' from Pallet a few years back that did exceedingly well in the Indigo League?" she asked.

"Must be the same guy," Lance agreed. "How did the kid fare?" He asked Sabrina.

Sabrina rubbed the bridge of her nose, and Lance and the others knew at once that whatever was coming next would be serious. "This creature, the one that attacked…it murdered one of Red's Pokemon. It didn't kill it for food, it murdered it in cold blood."

"Red must be taking it pretty hard," Brock sighed.

"Indeed," Sabrina said with a nod. "In fact, he has set out to find this creature, most likely for revenge."

"That's too dangerous," Flannery shouted. "Doesn't this kid know that this thing could kill the rest of his Pokemon, too?"

"Don't count Red out yet," Lance said while rubbing his chin. "He's a very powerful and determined trainer, and I doubt that he'll be caught off guard like that again. Besides, this might be exactly what we need. With Red chasing after this creature, we have more freedom to focus our resources towards this 'Pokemon god' and his cult."

No one seemed to disagree…


	4. Chapter 3: Fall From Grace

**Disclaimer:** I do not own Pokemon or any of their characters. I do however claim ownership of my variations of the charactersRed, Blue, Green, Yellow, and the "Pokemon god" as well as the storyline. 

(A/N): I really like this chapter. I don't know why though. Anyway, here we get our first glimpse at Green and Yellow and we get to see if the Pokemon godis all he claims to be.Reviews are greatly appreciated. You have no idea how much drive you get from one good review. R&R. Enjoy.

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**Chapter 3: Fall From Grace**

Green pulled his jacket tighter around his body and raised his hood to help block the cold wind. Green was an accomplished trainer of eighteen years old. He had short, spiky brown hair and very defined facial features.

"I hate this stupid weather," He growled as he hitched his jacket higher. "Why do we have to be at this stupid place?" he wondered, referring to the Sky Pillar.

"C'mon, Green," the sixteen year-old blonde girl by his side insisted. "You promised you'd be open minded." The girl was mid-level trainer named Yellow.

"I just can't believe you convinced me to travel all the way out here to Hoenn just to list this lunatic," he snapped.

"Be quiet," Yellow shushed with a quick look around to make sure no one had heard Green. "This guy is extremely sensitive about people questioning his sanity."

"Shouldn't that tell you something?" Green then asked rhetorically.

"But Green, you've seen what he's capable of doing," Yellow objected. "He's able to control both Groudon and Kyogre!"

"It's not the first time it's been done," Green pointed out. "Humans have managed to control the two titans before with the use of two orbs. And it's always turned out badly; Groudon and Kyogre have always ended up possessing whoever controls them."

"But he isn't using any orbs," Yellow protested. "He awakened them with just a wave of his hand! Besides, Groudon and Kyogre haven't even tried to fight each other, and their destructive tendencies are completely under his control."

"For now," Green muttered.

"He's starting!" Yellow exclaimed. She grabbed Green's hand and began to drag him forward towards where a tall man in a dark cloak was standing. Green allowed himself to be pulled.

On opposite sides of the man stood the two titanic Pokemon, Groudon and Kyogre (though Kyogre looked rather much like a beached whale in its current position). The two Pokemon and their apparent master stared into the dark, swirling sky with unwavering eyes. Then the man raised his arms and began to speak.

"_Oh great Sky Lord_,_ most noble of all dragons_," the man called out to the sky. "_Your master summons you here_. _Come to me_, _mighty Sky Lord_. _Come to me_, _Rayquaza_."

Green and Yellow waited expectedly for something to happen, but as the seconds turned to minutes, Green began to grow frustrated. "Told you this guy was a nutcase," Green laughed and turned to leave. But a monstrous roar stopped him in his tracks. Green spun around just as the mighty green dragon Rayquaza descended from the sky. It landed gently before the cloaked man and it almost looked as if the titanic beast bowed its head.

"Dear God," Green gasped. "That's Rayquaza! In all of the past two hundred years there have been only four confirmed sightings of it!" he said, showing his extensive knowledge of history and Pokemon in general.

"I told you," Yellow said with a proud smile. "This guy is the real deal."

"A real Pokemon god," Green agreed with wide eyes.

The Pokemon god turned and raised his arms up to the sky as the clouds parted. All around him his followers cheered and sang his praises while the three titans behind him roared in approval…


	5. Chapter 4: Alliance of Legends

**Disclaimer:** I do not own Pokemon or any of their characters. I do however claim ownership of my variations of the characters Red, Blue, Green, Yellow, and the "Pokemon god" as well as the storyline.

(A/N): I really enjoyed writing this chapter. Having to put actual personalitiesand dialect into a Pokemon was way more interesting and fun than just having them speak their names (plus that would be way harder to understand). Reviews are appreciated. R&R everybody. Enjoy.

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**Chapter 4: Alliance of Legends**

**----------Interlude: One month later----------**

The large eyes of a small, pink, cat-like Pokemon shifted towards the East. Mew slowly floated down through the mountains and over the trees of a forest before flying out over the ocean. Beneath Mew, a large dark shape began to come into focus as Lugia rose from the depths of the ocean to fly next to his longtime comrade.

"I take it that you have felt the disturbances as well?" Lugia asked as it soared alongside Mew. None of the Legendaries were capable of true spoken words, but they could communicate with any other living being through telepathy.

"Yes," Mew answered. Its "voice" was feminine and soft, almost playful. But the underlying seriousness was impossible to miss. "Groudon and Kyogre have been reawakened and Rayquaza has returned from the stratosphere once again."

"This isn't necessarily a bad thing," Lugia pointed out in his smooth, deep voice. "Maybe it is time that they rejoin us in protecting this world."

"No," Mew insisted. "I sense that something has gone terribly wrong. There is a dark, oppressive force within their minds. Something terrible is in the works."

Ho-oh and Celebi flew up beside Mew and Lugia. "Are you aware of Deoxys' return?" Ho-oh asked. "Perhaps it is he who causes these problems."

"I don't believe so," Celebi disagreed. "Deoxys' motives are completely unknown. In fact, we don't even know how sentient he really is. No, whatever has reawakened Groudon and Kyogre is a force far more sinister than Deoxys."

"Nevertheless, someone should go to get Deoxys back under control," Ho-oh suggested. "He has been on a destruction spree for the better part of a month." The four Legendaries came to a stop and they floated in the air, contemplating their next moves.

"I'll go," Mew decided. "Deoxys needs to be stopped."

"Wait," Lugia sighed. "I'll go instead. We need you here to keep an eye on what's going on with Kyogre, Groudon, and Rayquaza."

Ho-oh nodded her head in agreement. "Might I suggest looking to the humans for the source of this problem?" the great bird suggested. Lugia, Celebi, and Mew looked at her in shock. "Listen, hear me out first. For the past few months, I've been keeping track of a group of humans that keeps growing in size. The leader of this group is a man that claims to be a Pokemon god. This man's followers continue to grow in number and he preaches a unified world under his supreme control."

"Do you truly believe him to be the cause of the problems?" Mew asked. "This man would not be the first human to make such claims."

"This is true," Ho-oh agreed. "But this is the only man that I know of who holds such terrifying energy. Oh, and did I mention that he keeps Rayquaza, Groudon, and Kyogre as his company?"

"That would have been a helpful piece of information for you to have told us from the start," Lugia said, slightly annoyed. "But why haven't we been able to pick up on this?"

"I only happened upon him by chance," Ho-oh explained. "I forget when I first became aware of his presence, but ever since then I've kept my eye on him," she said. "The thing is, I've only been able to find him by looking for him specifically."

"I'll look into this," Mew nodded. "In the meantime, Ho-oh, I want you to take yours and Lugia's covens and keep watch for anything threatening."

"Such as?" Ho-oh inquired.

"Such as Kyogre and Groudon wreaking havoc on the entire world with their weather altering abilities," Mew answered. "You are to stop them no matter what." Ho-oh nodded and with a flap of her magnificent wings, the multi-colored bird departed from her fellow Legendaries and flew of into the sky.

"I'll go find Deoxys," Lugia stated. "Let's see if I can 'convince' him to leave." Lugia tucked in his wings and dropped into the ocean as he went of in search of Deoxys.

"I'll go investigate this so-called 'god'," Mew decided. She turned to Celebi. "Gather the Regis and wait for my return. I'll contact you periodically with news."

Celebi nodded. "Is there anything else that I could do?" she asked. "I don't like feeling useless."

"I understand," Mew said with furrowed brows. "Somehow your abilities to travel through time have been prevented, and I need someone to keep an eye on things for me. However, perhaps you could locate Latios and Latias." Celebi nodded in understanding. "Tell them what is happening and see if they are willing to help us."

Celebi nodded her understanding and flew off towards the South, where Latios and Latias usually resided. Mew then turned and flew off towards Kanto, where she would begin her search for the so-called Pokemon god…


	6. Chapter 5: Old Friends are New Enemies

**Disclaimer:** I do not own Pokemon or any of their characters. I do however claim ownership of my variations of the characters Red, Blue, Green, Yellow, Gold, Silver,and the "Pokemon god" as well as the storyline.

(A/N): Sorry for the relatively long wait, but the lack of reviews kinda slowed me down. But don't worry, I'm not abandoning this in the least. **_Please _R&R**. Enjoy

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"Slow down," Blue pleaded as Red sprinted ahead. "C'mon Red, wait up!" When they had heard explosions coming from the town ahead of them Red had immediately picked up his pace in hopes that the mysterious attacker (Deoxys) was the cause.

"I don't have that option," Red panted back as he continued to widen the gap between them. It had been an entire month since Red and Blue had set out to find their attacker, and while they had been able to follow the destruction left in his wake, they were unable to even catch another glimpse of him. Red was growing desperate.

Red burst from the forest into the main town square just in time to see the end of a vicious Pokemon battle. The powerful bear-like Ursaring had a bloody and beaten Scyther in its jaws. The much larger Ursaring was shaking its head violently as the Scyther wailed in pain. Finally the Ursaring released its opponent and threw it to the ground. Its trainer rushed to its side.

"Do you understand now?" a voice snarled from behind the Ursaring. A sixteen year-old boy with long, red hair stepped out from behind it. "Do you understand what happens when you refuse to obey the Master?" His Ursaring added a roar of its own as it advanced on the fallen Pokemon and its trainer.

"Silver?" Red whispered. He had met Silver some years ago and they had traveled together with their friends for quite a while. Silver had always been somewhat rude and had a superior attitude, but Red would never have suspected that the boy was capable of something as horrible as the sight before him.

Silver's Ursaring continued its advance on the Scyther and its trainer, when suddenly a fiery form burst from behind one of the storage sheds and slammed into the Ursaring. The great bear tumbled back as the Typhlosion that attacked it prepared to attack again.

"Gold!" Silver roared out in anger. Red immediately recognized Gold as another one of his traveling companions from years past. Gold was a dark-haired young man just one year younger than Red himself and the two had formed a strong friendship.

Silver's Ursaring rose to its feet and snarled at its smaller opponent, but Gold's Typhlosion refused to back down and the wolverine-like Pokemon roared back in defiance.

"How do you allow yourself to do this?" Gold demanded. "When does your conscience decide to shut itself off and let you maim and kill Pokemon and their trainers?"

"This man refused to obey the will of the Master!" Silver shouted back while pointing to the young man and his Scyther. "For this he must be punished."

"Listen to yourself," Gold demanded. "You sound like a raving lunatic. And while we're talking about raving lunatics, that Master of yours is a nutcase!"

Silver seethed with rage and ordered his Ursaring to attack. But Red had already seen and heard enough. He grabbed a Pokeball and released his Snorlax, which charged forward and tackled the much lighter Ursaring, throwing it to the ground.

"That's quite enough, Silver," Red declared as he stepped out of the underbrush. "Why don't you leave these people alone and find someone else to bother?" Red hissed.

"I see that the odds are against me," Silver sneered. He recalled his Ursaring and sent out his Murkrow. The black bird cawed once before Silver jumped on its back. "We'll meet again, Gold, Red," he snarled and then took off on the back of his Pokemon.

Red and Gold stood by each other as they watched Silver fly away. "What was that all about?" Red asked. "I thought the two of you had moved past your differences."

"We did," Gold said, still not taking his eyes off the sky. "But ever since Silver joined that cult things have changed. And now, now he spends most of his time beating up on other trainers."

"What a lowlife," Blue said as she ran up to them, still panting. "What kind of cult did that moron join?"

Gold looked at Blue and Red as if they had three heads. "You're kidding, right?" He asked incredulously. "It's that cult led by the guy claiming to be the god of all Pokemon." But Red and Blue continued to stare at Gold questioningly. "You really don't know about it? Have you been living under a rock for the past month? Hell, Silver isn't the only one of our group to join it."

"What are you saying?" Red asked.

"I'm saying that our 'good friends', Green and Yellow are part of that lunatic cult, too," Gold said in exasperation. "Man, where have you guys been for the past month?"

"We've been hunting down this…Pokemon, I guess," Red answered. "Though I'm not sure what it really was."

"Hell of a time to try and catch a rare Pokemon," Gold muttered. "This cult has the entire Pokemon League up in arms."

"I'm not looking to catch this thing," Red said with determination. At Gold's questioning look he continued, "It killed Poliwrath," he spat.

"Oh, man," Gold whispered. "I'm so sorry."

"There was no way you could have known," Red sighed. "But about this cult, why is it so powerful?"

"You're really clueless, aren't you?" Gold asked. "Sorry, I just can't believe that you haven't heard about this."

"So stop fooling around and spill the beans," Blue hissed, starting to get upset. She crossed her arms and waited for Gold's explanation with a slight narrowing of her eyes.

"As impatient as ever I see," Gold muttered. "This cult is run by a man who is claiming to be a Pokemon god," he said.

"We know that part," Blue interrupted.

"Man, you are really impatient!" Gold exclaimed. "Listen good, 'hot pants', while I'm telling the story you can keep your mouth shut or find someone else to tell you, alright?" Blue merely huffed in frustration. "Good. Now listen quick. This cult is huge, and I'm talking huge. It goes deeper than just one region and its more than just a few lousy trainers. This cult has six Gym Leaders from various gyms around Kanto, Johto, and Hoenn." Red and Blue gasped. "But that's not all. It's also got half of Hoenn's Elite Four and the current Hoenn Champion, Wallace."

"This is serious stuff," Red said thoughtfully.

"What makes it worse is that the cult leader is preaching the 'take over the world' thing," Gold said. "We know that the Pokemon League has some inside people, and they've reported that this guy is almost ready to wage open war on the entire world."

"Are you serious?" Blue exclaimed. "He would need an entire army for that to be done."

"He's got an army," Gold stated. "He has thousands of followers, all the resources of Team Rocket, and three ultra-powerful Pokemon on his side."

"What kind of Pokemon?" Red demanded, immediately thinking of the strange attacker.

"You wouldn't believe me if I told you," Gold said with a shake of his head. "He has control over the Trinity: Groudon, Kyogre, and Rayquaza."

"Shut the hell up," Red said, almost panicking. "There's no way."

"Believe it," Gold said. "But listen, if the two of you would be willing to help me out, I'd really appreciate it," Gold offered. "I've been outnumbered lately, and there's been a few times where I've had to fight Green on my own."

"How'd you fare?" Red asked.

"Not good," Gold answered. "Green's Pokemon are still as powerful as I remember. But you've always been his better, or at least his equal, haven't you?"

"We were pretty evenly matched last time," Red stated. He closed his eyes, wondering what he should do. The events of Poliwrath's death played over and over in his mind. But so did the things he saw Silver do that day. "I'll help you," he declared.

"Red," Blue said gently. "What about-?"

"This first," Red stated firmly. "Face it, Blue. We haven't had any leads on that thing since we left Pallet. And Gold's case seems to affect the immediate future a great deal. We'll stop this cult first, then I'll avenge Poliwrath," Red declared. Gold and Blue nodded and the trio set off to meet with the leaders of the Pokemon League…


	7. Chapter 6: Lugia and Deoxys

(A/N): Sorry for the long wait guys. The chapter was stored here, but I just forgot about everything. Anyway. Not much for me to explain here, I don't own Pokemon...yada yada yada. R&R!

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Lugia coursed through the ocean with graceful ease as he continued to move toward Deoxys. Slowly Lugia began to rise from the ocean's depths and soar through the clear night air. The sky around him was dark and full of stars for miles around. The great ocean guardian expanded his consciousness with his psychic powers and located Deoxys once again. Lugia finally spotted his target with his eyes and surged forward and up, rising in front of Deoxys and halting the dangerous Pokemon in mid-flight.

"What is your business here, Deoxys?" Lugia demanded. "What you have done in the last month is inexcusable. Leave this world forever or suffer the consequences," the great guardian roared.

Deoxys did not seem to hear Lugia, or he didn't understand, or just decided to ignore the mighty Pokemon's words. Deoxys just continued to stare at Lugia with his cold, lifeless eyes. Lugia understood; the challenge had been issued.

Without warning Deoxys struck. He hurled himself forward with incredible speed and force and slammed his frame into Lugia's. But Lugia was many times his size and withstood the attack with little difficulty. Using one of his arm-like wings, Lugia backhanded Deoxys and sent the smaller Pokemon sailing through the air.

But Deoxys quickly righted himself and resumed his attack. In between his four tentacles he gathered a sphere of psychic power and hurled it at Lugia, but Lugia rolled around the attack and retaliated with a powerful _Aeroblast_. The attack struck Deoxys dead center and sent him spiraling towards the ocean's surface. Lugia dove to take chase but Deoxys once again managed to stop his fall and flew directly above the surface of the water, throwing up a water trail in his wake.

Deoxys seemed to attempt to flee from Lugia but the great guardian would not allow it and chased after him. Deoxys was extraordinarily fast and was easily able to outrun Lugia, but escape wasn't on his mind. Deoxys quickly doubled back and came up alongside Lugia. By the time Lugia realized this it was too late. Deoxys' massive psychic sphere careened into Lugia and sent him tumbling beneath the waves.

Now it was Deoxys' turn to give chase. He dove into the water in search of Lugia, but what he found wasn't what he expected. Lugia was ready and waiting for him, and as soon as Deoxys was in his sights, Lugia released a powerful _Thunder_ attack. The conductivity of the water insured the attack's accuracy and Deoxys visibly recoiled in pain. He raced to escape from the watery trap and flew high into the air. But Lugia was not far behind. When Deoxys turned around to reinitiate his attack, he was met with the broad side of Lugia's powerful tail and was sent hurtling through the air.

But Deoxys righted himself once again. Its hollow eyes bored into Lugia's as Deoxys began to shift forms. He became thin and slender as he entered the speed form. Lugia was taken aback by this transformation. He had never seen it before; it was apparently something Deoxys had learned during its time away.

Deoxys raced forward, his speed was at an unheard of level, but just before he struck Lugia, Deoxys transformed into his defense form. When this more massive form –combined with the incredible momentum gained from the speed form- slammed into Lugia, it sent the mighty guardian flying through the air.

Lugia and Deoxys crash-landed on an island nearly half of a mile away. Deoxys rose first, as Lugia was nearly embedded in the ground due to the force of the impact. Deoxys once again shirted forms, this time into its attack form. He lashed out at Lugia, whipping his larger opponent viciously. But Lugia was able to swing one of its wings and hurl Deoxys away. Lugia charged forward and slammed its skull into Deoxys, but Deoxys responded by wrapping its tentacles around Lugia's head and digging its "feet" into the ground as a standoff began. Lugia dug its hind claws into the ground and gripped the earth fast with its fingerlike appendages on its arms. The guardian's powerful shoulder muscles strained to push forward, but Deoxys had grown immensely in physical power…


	8. Chapter 7: Enter Nosferatu

(A/N): I'll put up everything I have, so once again, I don't own Pokemon. R&R&Enjoy.

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Rayquaza's eyes snapped open as he emerged from his trance. He had sensed the power of Deoxys and knew that his old nemesis had returned. The mighty green dragon slowly wound his way up to the top of the Sky Pillar, where his master observed the world.

"Lord," Rayquaza bowed as he spoke to the Pokemon god with his telepathy. Rayquaza's "voice" was deep and powerful as the rumbling of thunder. "There is somewhere I must be."

"And where is that?" the Pokemon god asked.

"Deoxys has returned," Rayquaza stated. "I must go and stop him."

"You two have some history, do you not?" his master inquired. "You and he did battle when he first came to this planet, correct?" Rayquaza nodded. "And who won this battle?"

"Neither of us, lord," Rayquaza answered. "The fight was ended and he left before a clear victor could be decided."

"Interesting," the Pokemon god contemplated. "Very well, you may go and do battle with Deoxys once again. But be warned, Rayquaza. You will receive no aid from me if the battle goes not in your favor."

"I understand, lord," Rayquaza bowed and then he took to the sky. He flew high into the stratosphere and soared towards the battleground of Lugia and Deoxys.

"Interesting," Mew mused as it invisibly observed Rayquaza's flight from the Sky Pillar. Mew turned her eyes towards the man whom Rayquaza seemed to take his commands from. He was a powerfully built man standing well over six feet tall. He had long black hair and pitch black eyes. His facial features were sharp and angular, almost as if he had been chiseled out of solid rock. He wore a long black cloak that whipped around him in the powerful winds on the top of Sky Pillar.

Mew realized with a start that aside from herself and this so-called god, the top of Sky Pillar was completely abandoned.

"So good of you to finally decide to visit me, Mew," the dark man smirked as he turned towards Mew. His black eyes seemed to gaze right through Mew's invisibility. Realizing that it was useless, Mew became visible once again.

"Whoever you are," Mew said calmly. "I insist that you release Rayquaza, Groudon, and Kyogre from your spell."

"You do not understand," the Pokemon god answered in an almost playful manner. "I do not have them under a spell. They follow my orders and bow before me all on their own free will."

"Liar," Mew said confidently. "I felt your hold over Rayquaza's mind and even now I feel you trying to control me as well."

"Very perceptive," the Pokemon god laughed. "It must have been too presumptuous of me to try and control the most powerful psychic Pokemon. Ah, but where are my manners? Allow me to introduce myself; I am Nosferatu, the god of all Pokemon. And very soon, this entire world will belong to me."

"How dare you," Mew hissed. Her pink psychic aura flared up and Mew charged towards Nosferatu. But Nosferatu needed merely to raise one arm and a massive black beam erupted from his hand, ripping through Mew's aura and throwing Mew of the edge of Sky Pillar.

"Fool," Nosferatu laughed. He turned to walk away, but before he took two steps, a powerful psychic blast struck him and he stumbled to the ground. He turned to see Mew floating in the air behind him. Nosferatu smirked at the chance to use his real powers and he and Mew prepared for battle…


	9. Chapter 8: Rayquaza Victorious?

(A/N): I'll put up everything I have, so once again, I don't own Pokemon. R&R&Enjoy.

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Lugia and Deoxys continued to struggle against each other but neither gained any ground as they remained locked together. As each strained to get the upper hand, a massive _Hyper Beam_ plummeted from the sky and crashed into both combatants. The force of the attack threw Lugia and Deoxys from each other.

Lugia's eyes scanned the sky and they fell upon Rayquaza. The massive green dragon hovered above him in the sky threateningly as it prepared to attack again. A second beam exploded from Rayquaza's mouth and crashed into Deoxys. Lugia shuddered at the power the green dragon possessed; the beam had completely engulfed Deoxys.

But Deoxys wasn't quite ready to stop fighting. He transformed into his attack form and charged towards Rayquaza. Deoxys' whip-like arms lashed out and smacked Rayquaza into the ground. A powerful sphere of psychic energy built up between Deoxys four tentacles and he prepared to launch it point blank into Rayquaza. But before Deoxys could attack, he was struck with Lugia's own psychic blast and was thrown away.

Lugia went to stand by Rayquaza, but the great dragon stuck with his glowing claws and slashed Lugia across the chest before breathing draconic flame onto the ancient sea guardian.

"This is my battle," Rayquaza roared. He hovered menacingly just above Lugia's prone form. "If you interfere again I'll rip you apart," the dragon threatened. But while his attention was directed towards Lugia, Deoxys struck. He slammed himself into Rayquaza and drove the dragon into the ground. A volley of harsh and heavy blows rained down upon Rayquaza and though the dragon was quickly able to fling Deoxys away, the damage had been done.

Rayquaza and Deoxys crashed together again, but just as they made contact a great torrent of water struck them and pressed them into the ground. Lugia's follow-up attack was a massive electrical discharge that coursed through both Rayquaza and Deoxys. Rayquaza sprang up first and roared in fury (as Lugia had interfered in his battle), but Lugia answered with a roar of its own and met Rayquaza's charge.

The two collided and fought for control. Rayquaza coiled his body around Lugia while Lugia repeatedly slammed Rayquaza into the ground. Lugia's psychic powers lashed out angrily and pressed on Rayquaza's mind. But Deoxys quickly lashed out at both opponents and rammed into Lugia's back sending Lugia and Rayquaza flying into a rock wall.

Rayquaza tossed Lugia's beaten form from atop him and turned to face Deoxys. The mighty dragon launched another _Hyper Beam_ at Deoxys, but Deoxys had already shifted to its defense form and the attack affected him considerably less. Deoxys then shifted back into his attack form and sped forward, but he didn't anticipate that Rayquaza would match his speed. Rayquaza caught Deoxys in his fiery claws and slammed him into the ground. The dragon then opened his great maw and breathed deadly fire upon Deoxys before throwing him out into the ocean…


	10. Chapter 9: The Legion of Nosferatu

(A/N): I'll put up everything I have, so once again, I don't own Pokemon. R&R&Enjoy.

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Nosferatu stood triumphantly over Mew's fallen form. The small pink Pokemon lay bruised and beaten at the god's feet. Nosferatu picked Mew up by the back of her neck and lifted her beaten and nearly unconscious body to the sky as a show of victory. He then made his way down the winding staircase of the Sky Pillar, Mew still in hand. He walked all the way down to the lowest basement level and entered a massive underground cavern. Within this cavern was a great pool of water that left the cavern through a submerged channel. There was also a massive tunnel through the cave walls that led to the surface. In the deep pool of water rested Kyogre, while Groudon slept at the entrance of the tunnel.

"Awaken, my beasts," Nosferatu commanded. "Your master commands you…awaken!" The eyes of Kyogre and Groudon snapped open and they both made their way towards Nosferatu. "Now we begin what we set out to do," Nosferatu stated. "You two will begin the assault on the nonbelievers and destroy their world!" Kyogre and Groudon seemed to bow their heads before they turned and left, Kyogre through the underwater channel, and Groudon through the tunnel.

The Pokemon god pondered what to do with Mew, whom he still held firmly in his grasp and suddenly an idea came to him. Nosferatu rose through rock and stone as if it were air and returned to the top of the Sky Pillar. He stretched his will of the stone and four claw-like structures curled up. He tossed Mew to the center of the four claws and then poured his power into them. Almost at once, a great field of power began to flow between and around them, trapping Mew inside. The mighty Mew, the unofficial leader of the legendaries, had become Nosferatu's prisoner.

Nosferatu turned and made his way to the base of the Sky Pillar to where his most loyal followers waited. True his influence spread across the entire world, but those followers most powerful and most loyal to him remained with Nosferatu at the Sky Pillar. Nosferatu stood before them regally and swept his arms out wide.

"It begins," he bellowed, his thundering with tremendous force. "The time for action is now. We will march across this world and make it our own! Our time has come!" Nosferatu's speech elicited a tremendous war cry from his followers, but his voice did not remain solely at the Sky Pillar. Nosferatu's voice flowed into the minds of his followers all over the world. And they heard his message. And they prepared for war. And the world was doomed…


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